Harold Pimentel
@hjp.bsky.social
Assistant prof at UCLA using the Bayes for the genomes https://pimentellab.com
Destroying the earth to make shit memes with GPT:
(the idea was not mine, fortunately)
(the idea was not mine, fortunately)
November 18, 2025 at 3:48 AM
Destroying the earth to make shit memes with GPT:
(the idea was not mine, fortunately)
(the idea was not mine, fortunately)
Reposted by Harold Pimentel
@jbenning.bsky.social @jedidiahcarlson.com
et al. exemplify how confounding can lead to flawed inference on genetic causality. In studies of human behavior and social outcomes, the cost of downplaying this problem can be steep. royalsocietypublishing.org/doi/epdf/10.... bsky.app/profile/jben...
et al. exemplify how confounding can lead to flawed inference on genetic causality. In studies of human behavior and social outcomes, the cost of downplaying this problem can be steep. royalsocietypublishing.org/doi/epdf/10.... bsky.app/profile/jben...
November 7, 2025 at 8:07 PM
@jbenning.bsky.social @jedidiahcarlson.com
et al. exemplify how confounding can lead to flawed inference on genetic causality. In studies of human behavior and social outcomes, the cost of downplaying this problem can be steep. royalsocietypublishing.org/doi/epdf/10.... bsky.app/profile/jben...
et al. exemplify how confounding can lead to flawed inference on genetic causality. In studies of human behavior and social outcomes, the cost of downplaying this problem can be steep. royalsocietypublishing.org/doi/epdf/10.... bsky.app/profile/jben...
Reposted by Harold Pimentel
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
October 14, 2025 at 8:48 PM
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
Reposted by Harold Pimentel
The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert)
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
October 7, 2025 at 9:20 PM
The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert)
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
Reposted by Harold Pimentel
The first (of hopefully many) reports to come from our collaboration with @hjp.bsky.social
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
September 30, 2025 at 7:17 PM
The first (of hopefully many) reports to come from our collaboration with @hjp.bsky.social
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
September 29, 2025 at 4:47 PM
Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
Reposted by Harold Pimentel
Harvard Dean Was Paid $150,000 as an Expert Witness in Tylenol Lawsuits
www.nytimes.com
September 24, 2025 at 1:29 AM
Super excited to have this out. Thanks very much to the reviewers who helped improve this manuscript. Congrats to @jingyour.bsky.social!
bsky.app/profile/bioi...
bsky.app/profile/bioi...
🧩 Recently published in Bioinformatics Advances: “Rosace-AA: Enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights”
Full article available: https://doi.org/10.1093/bioadv/vbaf218
Full article available: https://doi.org/10.1093/bioadv/vbaf218
September 22, 2025 at 5:35 PM
Super excited to have this out. Thanks very much to the reviewers who helped improve this manuscript. Congrats to @jingyour.bsky.social!
bsky.app/profile/bioi...
bsky.app/profile/bioi...
Pretty sure that’s the point bsky.app/profile/josh...
"Losses of significant research and other federal funding would devastate UC and inflict real, long-term harm on our students, faculty, staff, patients, and all Californians. It would also end life-saving research from which all Americans benefit."
www.universityofcalifornia.edu/press-room/l...
www.universityofcalifornia.edu/press-room/l...
September 15, 2025 at 6:26 PM
Pretty sure that’s the point bsky.app/profile/josh...
Reposted by Harold Pimentel
BREAKING: Trump, Hegseth violated the Posse Comitatus Act with their troop deployment to Los Angeles, Judge Charles Breyer rules after trial. storage.courtlistener.com/recap/gov.us...
September 2, 2025 at 1:50 PM
BREAKING: Trump, Hegseth violated the Posse Comitatus Act with their troop deployment to Los Angeles, Judge Charles Breyer rules after trial. storage.courtlistener.com/recap/gov.us...
Reposted by Harold Pimentel
You’re not dropping a single, asshole.
If you’re actually knew anything, it would be criminal not to reveal it now. But of course, this is a bullshit publicity stunt.
If you’re actually knew anything, it would be criminal not to reveal it now. But of course, this is a bullshit publicity stunt.
August 27, 2025 at 2:41 AM
You’re not dropping a single, asshole.
If you’re actually knew anything, it would be criminal not to reveal it now. But of course, this is a bullshit publicity stunt.
If you’re actually knew anything, it would be criminal not to reveal it now. But of course, this is a bullshit publicity stunt.
Reposted by Harold Pimentel
i imagine this implicitly anti-newsom flyer is showing up on doorsteps across california.
'visit protectfairelections.org to learn more,' it says. 'paid for by Right Path Coalition'.
which is . . . led by the chairperson of the california republican party
'visit protectfairelections.org to learn more,' it says. 'paid for by Right Path Coalition'.
which is . . . led by the chairperson of the california republican party
August 26, 2025 at 11:44 PM
i imagine this implicitly anti-newsom flyer is showing up on doorsteps across california.
'visit protectfairelections.org to learn more,' it says. 'paid for by Right Path Coalition'.
which is . . . led by the chairperson of the california republican party
'visit protectfairelections.org to learn more,' it says. 'paid for by Right Path Coalition'.
which is . . . led by the chairperson of the california republican party
Reposted by Harold Pimentel
From @jxtxfoundation.bsky.social | JXTX + CSHL 2025 Genome Informatics Scholarships | Up to $750 for domestic or $1,250 for international travel | Application deadline is September 15, 2025 | #OpenScience 🧬 🖥️ 🧪
⬇️
jxtxfoundation.org/news/2025-6-...
⬇️
jxtxfoundation.org/news/2025-6-...
JXTX + CSHL 2025 Genome Informatics Scholarship
JXTX + CSHL 2025 Genome Informatics Scholarships
jxtxfoundation.org
August 26, 2025 at 2:13 PM
From @jxtxfoundation.bsky.social | JXTX + CSHL 2025 Genome Informatics Scholarships | Up to $750 for domestic or $1,250 for international travel | Application deadline is September 15, 2025 | #OpenScience 🧬 🖥️ 🧪
⬇️
jxtxfoundation.org/news/2025-6-...
⬇️
jxtxfoundation.org/news/2025-6-...
Reposted by Harold Pimentel
Y'all
The ICE building in Portland is painting a line in front of their building
But they don't even know how to spell government
The ICE building in Portland is painting a line in front of their building
But they don't even know how to spell government
August 23, 2025 at 6:25 PM
Y'all
The ICE building in Portland is painting a line in front of their building
But they don't even know how to spell government
The ICE building in Portland is painting a line in front of their building
But they don't even know how to spell government
Reposted by Harold Pimentel
Science will always be political when it tries to help people who the political establishment doesn't center as the default American.
Health disparities? Climate change? Public health?
Have always been political, will always be political.
Health disparities? Climate change? Public health?
Have always been political, will always be political.
Insisting on expertise over ideology is not “politicizing” science. The ideologues installing scientific and governmental policy that is contradicted by evidence and data are.
By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.
By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.
Scientists Are Caught in a Political Trap
Fighting back against the Trump administration means they start to look more like activists.
www.theatlantic.com
August 23, 2025 at 6:08 PM
Science will always be political when it tries to help people who the political establishment doesn't center as the default American.
Health disparities? Climate change? Public health?
Have always been political, will always be political.
Health disparities? Climate change? Public health?
Have always been political, will always be political.
Reposted by Harold Pimentel
Yesterday the Supreme Court issued a convoluted, 36-page emergency order about NIH grant terminations. Two main takeaways:
-$2 billion (not the government # of $780 million) in NIH grants will likely be re-terminated
-future legal challenges will be much harder
w/ @maxkozlov.bsky.social:
-$2 billion (not the government # of $780 million) in NIH grants will likely be re-terminated
-future legal challenges will be much harder
w/ @maxkozlov.bsky.social:
US Supreme Court allows NIH to cut $2 billion in research grants
The decision will hinder lawsuits against grant terminations, legal specialists say.
www.nature.com
August 22, 2025 at 6:21 PM
Yesterday the Supreme Court issued a convoluted, 36-page emergency order about NIH grant terminations. Two main takeaways:
-$2 billion (not the government # of $780 million) in NIH grants will likely be re-terminated
-future legal challenges will be much harder
w/ @maxkozlov.bsky.social:
-$2 billion (not the government # of $780 million) in NIH grants will likely be re-terminated
-future legal challenges will be much harder
w/ @maxkozlov.bsky.social:
Reposted by Harold Pimentel
Very proud of @ytchang11.bsky.social for her first publication from her doctoral research! She conducted very meticulous genomic analyses that uncovered novel isoform-specific mechanistic hypotheses underlying genetic loci associated with multiple cancers.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level - British Journal of Cancer
British Journal of Cancer - Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level
www.nature.com
August 20, 2025 at 9:09 PM
Very proud of @ytchang11.bsky.social for her first publication from her doctoral research! She conducted very meticulous genomic analyses that uncovered novel isoform-specific mechanistic hypotheses underlying genetic loci associated with multiple cancers.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Very excited to have this out! Here, we take inspiration from model selection MR to decouple direct and indirect effects in DMS experiments. Check out Jingyou's explainer and paper below:
bsky.app/profile/jing...
bsky.app/profile/jing...
How do we decouple the effects of two functional phenotypes in protein deep mutational scanning (DMS)?
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions
Multi-phenotype deep mutational scanning (DMS) experiments provide a powerful means to dissect how protein variants affect different layers of molecular function, such as abundance, surface expression...
www.biorxiv.org
August 15, 2025 at 4:22 PM
Very excited to have this out! Here, we take inspiration from model selection MR to decouple direct and indirect effects in DMS experiments. Check out Jingyou's explainer and paper below:
bsky.app/profile/jing...
bsky.app/profile/jing...
Reposted by Harold Pimentel
Reposted by Harold Pimentel
It is depressing, but all too predictable, how swiftly we’ve gone from the Social Science Genetic Association Consortium offering reassurances about the uses of behavioural polygenic scores to one of their lead authors marketing embryo selection for IQ
August 2, 2025 at 2:15 AM
It is depressing, but all too predictable, how swiftly we’ve gone from the Social Science Genetic Association Consortium offering reassurances about the uses of behavioural polygenic scores to one of their lead authors marketing embryo selection for IQ
Reposted by Harold Pimentel
Suspension of all grants to UCLA www.latimes.com/california/s...
Trump freezes $200 million in UCLA science and medical research funding, citing antisemitism
The Trump administration has frozen roughly $200 million in National Science Foundation, National Institutes of Health and other federal agency-funded research at UCLA, citing allegations the school d...
www.latimes.com
August 1, 2025 at 4:27 AM
Suspension of all grants to UCLA www.latimes.com/california/s...
Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...
Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social
July 21, 2025 at 11:15 PM
Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...
Reposted by Harold Pimentel
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
📢OUT TODAY @natgenet.nature.com
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk - Nature Genetics
SuShiE is a multiancestry fine-mapping method for molecular quantitative trait loci that leverages linkage disequilibrium heterogeneity to improve resolution, infer cross-ancestry effect size correlat...
www.nature.com
July 21, 2025 at 6:54 PM
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
Reposted by Harold Pimentel
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon